plot.anomalyZone: plot.anomalyZone

In chutter/FilterZone: R Package For Detecting the Anomaly Zone and Alignment Filtering in Large Phylogenomic Datasets

Description

Function for plotting data collected for the anomaly zone

Usage

## S3 method for class 'anomalyZone'
plot(
  tree = NULL,
  data = NULL,
  outgroups = NULL,
  save.file = NULL,
  tip.label.size = 0.5,
  node.label.size = 1,
  edge.width = 3
)

Arguments

tree	Tree that you wish to plot
data	data.table from the anomalyZone function
outgroups	provide outgroups for rooting plotted tree
save.file	if you wish to save to file, put file name. Saves as PDF
tip.label.size	size of the tip labels, passed to cex in plotting function
node.label.size	size of the node label circles, passed to cex in plotting function
edge.width	size of the branch edges, passed to edge.width in plot.phylo

Value

plots the phylogenetic tree and selected data associated with an AstralPlane object. Can optionally be saved to file as a PDF by giving save.file a file name.

Examples

your.tree = ape::read.tree(file = "file-path-to-tree.tre")
astral.data = astralPlane(astral.tree = your.tree,
                          outgroups = c("species_one", "species_two"),
                          tip.length = 1)

chutter/FilterZone documentation built on Dec. 19, 2021, 4:07 p.m.